sak - Online in the Cloud

PROGRAM:

NAME

sak - Slicing and dicing of FASTA/FASTQ files..

SYNOPSIS

sak [OPTIONS] [\B-o OUT.{fa,fq}] IN.{fa,fq}

DESCRIPTION

"It slices, it dices and it makes the laundry!"

Rewrite of the original SAK tool by Manuel Holtgrewe.

-h, --help

Displays this help message.

--version

Display version information

Output Options:

-o, --out-path FASTX

Path to the resulting file. If omitted, result is printed to stdout. Use files
ending in .fq or . to write out FASTQ. Valid filetypes are: .fq, .fastq, .fa,
.fasta, .faa, .ffn, .fna, and .frn.

-rc, --revcomp

Reverse-complement output.

-l, --max-length LEN

Maximal number of sequence characters to write out.

Filter Options:

-s, --sequence NUM

Select the given sequence for extraction by 0-based index.

-sn, --sequence-name NAME

Select sequence with name prefix being NAME.

-ss, --sequences RANGE

Select sequences from-to where from and to are 0-based indices.

-i, --infix RANGE

Select characters from-to where from and to are 0-based indices.

-ll, --line-length LEN

Set line length in output file. See section Line Length for details. In range
[-1..inf].

LINE LENGTH

You can use the setting --line-length for setting the resulting line length. By
default, sequences in FASTA files are written with at most 70 characters per line
and sequences in FASTQ files are written without any line breaks. The quality
sequence in FASTQ file is written in the same way as the residue sequence.

The default is selected with a --line-length value of -1 and line breaks can be
disabled with a value of 0.

USAGE EXAMPLES

sak -s 10 IN.fa

Cut out 11th sequence from IN.fa and write to stdout as FASTA.

sak -ss 10-12 -ss 100-200 IN.fq

Cut out 11th up to and including 12th and 101th up to and including 199th sequence
from IN.fq and write to stdout as FASTA.

VERSION

sak version: 0.2 Last update November 2012

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